diff --git a/DESCRIPTION b/DESCRIPTION index 558e0511f..20d4dcc83 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.4.0.9013 +Version: 1.4.0.9014 Date: 2020-11-09 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index e8f2d7557..37ef27a56 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.4.0.9013 +# AMR 1.4.0.9014 ## Last updated: 9 November 2020 ### New diff --git a/R/mo.R b/R/mo.R index 08fb4a32e..026846c3c 100755 --- a/R/mo.R +++ b/R/mo.R @@ -1417,7 +1417,7 @@ exec_as.mo <- function(x, # - Becker et al. 2014, PMID 25278577 # - Becker et al. 2019, PMID 30872103 # - Becker et al. 2020, PMID 32056452 - post_Becker <- c("") # 2020-10-20 currently all are mentioned in above papers + post_Becker <- character(0) # 2020-10-20 currently all are mentioned in above papers if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) { warning("Becker ", font_italic("et al."), " (2014, 2019) does not contain these species named after their publication: ", diff --git a/R/mo_property.R b/R/mo_property.R index 7011fe069..ca1375de8 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -140,9 +140,11 @@ #' language = "nl") # "Streptococcus groep A" #' #' # gram stains can be used as a filter -#' example_isolates %>% -#' filter(is_gram_positive()) -#' +#' if (require("dplyr")) { +#' example_isolates %>% +#' filter(is_gram_positive()) +#' } +#' #' # other -------------------------------------------------------------------- #' # get a list with the complete taxonomy (from kingdom to subspecies) #' mo_taxonomy("E. coli") diff --git a/R/sysdata.rda b/R/sysdata.rda index 00d266a66..736d43dc1 100644 Binary files a/R/sysdata.rda and b/R/sysdata.rda differ diff --git a/docs/404.html b/docs/404.html index e697ec40c..a151962d6 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 88ded8814..e56c6da9e 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014 diff --git a/docs/articles/index.html b/docs/articles/index.html index 36ecae2e1..ebcd72b00 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014 diff --git a/docs/authors.html b/docs/authors.html index b01618bef..df3c87175 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014 diff --git a/docs/index.html b/docs/index.html index fb58e2cc3..52a846e87 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014 diff --git a/docs/news/index.html b/docs/news/index.html index ad9a4558a..495519dce 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.4.0.9013 Unreleased +
+

+AMR 1.4.0.9014 Unreleased

@@ -252,7 +252,7 @@

Functions is_gram_negative() and is_gram_positive() as wrappers around mo_gramstain(). They always return TRUE or FALSE (except when the input is NA or the MO code is UNKNOWN), thus always return FALSE for species outside the taxonomic kingdom of Bacteria. If you have the dplyr package installed, they can even determine the column with microorganisms themselves inside dplyr functions:

 example_isolates %>%
-  filter(is_gram_positive())
+  filter(is_gram_positive())
 #> NOTE: Using column `mo` as input for 'x'

  • Functions %not_like% and %not_like_case% as wrappers around %like% and %like_case%. The RStudio addin to insert the text " %like% " as provided in this package now iterates over all like variants. So if you have defined the keyboard shortcut Ctrl/Cmd + L to this addin, it will first insert %like% and by pressing it again it will be replaced with %not_like%, etc.

    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 4bc7fd58b..353707ece 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2020-11-09T12:06Z +last_built: 2020-11-09T14:18Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index aa5dedce2..4e6868472 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014

    diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index b5bac64e3..73e65ea86 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -82,7 +82,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014
    @@ -479,8 +479,10 @@ This package contains the complete taxonomic tree of almost all microorganisms ( language = "nl") # "Streptococcus groep A" # gram stains can be used as a filter -example_isolates %>% - filter(is_gram_positive()) +if (require("dplyr")) { + example_isolates %>% + filter(is_gram_positive()) +} # other -------------------------------------------------------------------- # get a list with the complete taxonomy (from kingdom to subspecies) diff --git a/docs/survey.html b/docs/survey.html index 6f52806c0..31c23b778 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.4.0.9013 + 1.4.0.9014

    diff --git a/man/mo_property.Rd b/man/mo_property.Rd index dc4a2beeb..c3b99514a 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -259,8 +259,10 @@ mo_fullname("S. pyogenes", language = "nl") # "Streptococcus groep A" # gram stains can be used as a filter -example_isolates \%>\% - filter(is_gram_positive()) +if (require("dplyr")) { + example_isolates \%>\% + filter(is_gram_positive()) +} # other -------------------------------------------------------------------- # get a list with the complete taxonomy (from kingdom to subspecies)